Genetic bias in repeated evolution of pigment loss in cave populations of the Asellus aquaticus species complex

Similar phenotypes can evolve repeatedly under the same evolutionary pressures. A compelling example is the evolution of pigment loss and eye loss in cave-dwelling animals. While specific genomic regions or genes associated with these phenotypes have been identified in model species, it remains uncertain whether a bias towards particular genetic mechanisms exists. An isopod crustacean, Asellus aquaticus, is an ideal model organism to investigate this phenomenon. It inhabits surface freshwaters throughout Europe but has colonized groundwater on multiple independent occasions and evolved several cave populations with distinct ecomorphology. Previous studies have demonstrated that three different cave populations utilized common genetic regions, potentially the same genes, in the evolution of pigment and eye loss. Expanding on this, we conducted analysis on two additional cave populations, distinct either phylogenetically or biogeographically from those previously examined. We generated F2 hybrids from cave × surface crosses and tested phenotype-genotype associations, as well as conducted complementation tests by crossing individuals from different cave populations. Our findings revealed that pigment loss and orange eye pigment in additional cave populations were associated with the same genomic regions as observed in the three previously tested cave populations. Moreover, the lack of complementation across all cross combinations suggests that the same gene likely drives pigment loss. These results substantiate a genetic bias in the recurrent evolution of pigment loss in this model system. Future investigations should focus on the cause behind this bias, possibly arising from allele recruitment from ancestral surface populations' genetic variation or advantageous allele effects via pleiotropy.

Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome

Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.

A practical guide for the husbandry of cave and surface invertebrates as the first step in establishing new model organisms

While extensive research on traditional model species has significantly advanced the biological sciences, the ongoing search for new model organisms is essential to tackle contemporary challenges such as human diseases or climate change, and fundamental phenomena including adaptation or speciation. Recent methodological advances such as next-generation sequencing, gene editing, and imaging are widely applicable and have simplified the selection of species with specific traits from the wild. However, a critical milestone in this endeavor remains the successful cultivation of selected species. A historically overlooked but increasingly recognized group of non-model organisms are cave dwellers. These unique animals offer invaluable insights into the genetic basis of human diseases like eye degeneration, metabolic and neurological disorders, and basic evolutionary principles and the origin of adaptive phenotypes. However, to take advantage of the beneficial traits of cave-dwelling animals, laboratory cultures must be established-a practice that remains extremely rare except for the cavefish Astyanax mexicanus. For most cave-dwelling organisms, there are no published culturing protocols. In this study, we present the results of our multi-year effort to establish laboratory cultures for a variety of invertebrate groups. We have developed comprehensive protocols for housing, feeding, and husbandry of cave dwellers and their surface relatives. Our recommendations are versatile and can be applied to a wide range of species. Hopefully our efforts will facilitate the establishment of new laboratory animal facilities for cave-dwelling organisms and encourage their greater use in experimental biology.

Sex-dependent increase of movement activity in the freshwater isopod Asellus aquaticus following adaptation to a predator-free cave habitat

Populations experiencing negligible predation pressure are expected to evolve higher behavioral activity. However, when sexes have different expected benefits from high activity, the adaptive shift is expected to be sex-specific. Here, we compared movement activity of one cave (lack of predation) and three adjacent surface (high and diverse predation) populations of Asellus aquaticus, a freshwater isopod known for its independent colonization of several caves across Europe. We predicted 1) higher activity in cave than in surface populations, with 2) the difference being more pronounced in males as they are known for active mate searching behavior, while females are not. Activity was assessed both in the presence and absence of light. Our results supported both predictions: movement activity was higher in the cave than in the surface populations, particularly in males. Relaxed predation pressure in the cave-adapted population is most likely the main selective factor behind increased behavioral activity, but we also showed that the extent of increase is sex-specific.

Individual level microbial communities in the digestive system of the freshwater isopod Asellus aquaticus: Complex, robust and prospective

The freshwater isopod Asellus aquaticus is an important decomposer of leaf detritus, and its diverse gut microbiome has been depicted as key contributors in lignocellulose degradation as of terrestrial isopods. However, it is not clear whether the individual-level microbiome profiles in the isopod digestive system across different habitats match the implied robust digestion function of the microbiome. Here, we described the bacterial diversity and abundance in the digestive system (hindgut and caeca) of multiple A. aquaticus individuals from two contrasting freshwater habitats. Individuals from a lake and a stream harboured distinct microbiomes, indicating a strong link between the host-associated microbiome and microbes inhabiting the environments. While faeces likely reflected the variations in environmental microbial communities included in the diet, the microbial communities also substantially differed in the hindgut and caeca. Microbes closely related to lignocellulose degradation are found consistently more enriched in the hindgut in each individual. Caeca often associated with taxa implicated in endosymbiotic/parasitic roles (Mycoplasmatales and Rickettsiales), highlighting a complex host-parasite-microbiome interaction. The results highlight the lability of the A. aquaticus microbiome supporting the different functions of the two digestive organs, which may confer particular advantages in freshwater environments characterized by seasonally fluctuating and spatially disparate resource availability.

Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution

BACKGROUND

Transcriptomic methods can be used to elucidate genes and pathways responsible for phenotypic differences between populations. Asellus aquaticus is a freshwater isopod crustacean with surface- and cave-dwelling ecomorphs that differ greatly in multiple phenotypes including pigmentation and eye size. Multiple genetic resources have been generated for this species, but the genes and pathways responsible for cave-specific characteristics have not yet been identified. Our goal was to generate transcriptomic resources in tandem with taking advantage of the species' ability to interbreed and generate hybrid individuals.

RESULTS

We generated transcriptomes of the Rakov Škocjan surface population and the Rak Channel of Planina Cave population that combined Illumina short-read assemblies and PacBio Iso-seq long-read sequences. We investigated differential expression at two different embryonic time points as well as allele-specific expression of F₁ hybrids between cave and surface individuals. RNAseq of F₂ hybrids, as well as genotyping of a backcross, allowed for positional information of multiple candidate genes from the differential expression and allele-specific analyses.

CONCLUSIONS

As expected, genes involved in phototransduction and ommochrome synthesis were under-expressed in the cave samples as compared to the surface samples. Allele-specific expression analysis of F₁ hybrids identified genes with cave-biased (cave allele has higher mRNA levels than the surface allele) and surface-biased expression (surface allele has higher mRNA levels than the cave allele). RNAseq of F₂ hybrids allowed for multiple genes to be placed to previously mapped genomic regions responsible for eye and pigmentation phenotypes. In the future, these transcriptomic resources will guide prioritization of candidates for functional analysis.

Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore ( Asellus aquaticus )

Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.

Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod, Asellus aquaticus

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F₂ crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.

Exploratory behaviour divergence between surface populations, cave colonists and a cave population in the water louse, Asellus aquaticus

Abstract

Behaviour is considered among the most important factors in colonising new habitats. While population divergence in behaviour is well-documented, intraspecific variation in exploratory behaviour in species with populations successfully colonising and adapting to extreme (compared to the ‘typical’) habitats is less understood. Here, by studying surface- vs. cave-adapted populations of water louse (Asellus aquaticus), we tested whether (i) adaptation to the special, ecologically isolated cave habitat includes a decrease in explorativeness and (ii) recent, surface-type cave colonists are more explorative than their surface conspecifics from the source population. We repeatedly tested dispersal related novel area exploration and dispersal speed in both the presence and absence of light. We found that surface populations showed higher behavioural activity in dark than in light, and they were more explorative and dispersed faster than their cave conspecifics. Recent colonists showed a trend of higher dispersal speed compared to their source surface population. We suggest that extreme and isolated habitats like caves might work as ‘dispersal traps’ following successful colonisation, because adaptation to these habitats includes the reduction of explorativeness. Furthermore, we suggest that individuals with higher explorativeness are likely to colonise markedly new environments. Finally, we provide experimental evidence about surface A. aquaticus moving more in dark than in light.

Significance statement

Environmental conditions in caves are differing drastically from those of the surface. Consequently, animals colonising subterranean habitats are subject to different selective forces than those experienced by the ancestral surface-living population. Behaviour is believed to be a key factor in successful colonisation to novel habitats; however, intraspecific behavioural variation in species with both surface- and cave-adapted populations is less known. Here, we compared dispersal related novel area exploration and dispersal speed across surface and cave-adapted populations of the freshwater crustacean Asellus aquaticus. Our results show that cave-adapted A. aquaticus are significantly less explorative and disperse slower than surface-type populations, indicating that caves may act as ‘dispersal traps’, where adaptation includes the loss of explorativeness. Also, recent cave colonists show a trend to be faster dispersers than peers from the surface source population, suggesting that individuals with higher explorativeness are likely to colonise markedly different new environments.

A new obligate groundwater species of Asellus (Isopoda, Asellidae) from Iran

With only 43 described stygobionts and only two isopod species the obligate groundwater fauna of Iran, a vast country with over 10% of limestone surface, is inadequately known. Here, we report the discovery of Asellus ismailsezarii sp. nov. from Zagros mountains, the first eyeless and depigmented asellid isopod from Iran. The new species is morphologically similar to Asellus monticola Birstein, 1932, but it is eyeless and fully depigmented, has a slightly curved pereopod IV and does not bear any setae on proximal margins of exopodite of pleopods IV and V. Species phylogenetic relationships using original and datamined mitochondrial DNA and nuclear rDNA, and estimation of molecular divergences with other Asellus species, suggest that A. ismailsezarii sp. nov. is sister to a larger clade that also contains the European A. aquaticus species complex. Surface populations of Asellus have colonized groundwater at multiple occasions and localities, both in Europe and Asia, giving rise to species and subspecies that have evolved troglomorphisms, such as depigmentation and loss of eyes. Of the 37 formally described species and subspecies of Asellus, 15 are from groundwater, including A. ismailsezarii sp. nov. We predict that many more obligate groundwater Asellus taxa are yet to be discovered in Asia.